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	<div> <i><font size="+1" color="#ffaa00"><b> Search full text, citations, references for (m)any
		       article(s)</b></font></i>
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<div id="imageLoc">
  <h1>List of items:</h1>
<ul id="navlist">
<li><a href="#23">Three flavors of CitationControl.</a></li>
<li><a href="#17">Starting CitationControl.</a></li>
<li><a href="#1">Setting preferences.</a></li>
<li><a href="#14">Indexing article pdf files in your
computer.</a></li>
<li><a href="#15">Open any pdf file in your database immediately.</a></li>
<li><a href="#16">Viewing images from articles in the database.</a></li>
<li><a href="#2">Performing an online search based on keywords,
authors, journal and years.</a></li>
<li><a href="#3">Obtaining citations and references.</a></li>
<li><a href="#18">Save and reload sessions of searches.</a></li>
<li><a href="#19">Export all articles to a bibliography file.</a></li>
<li><a href="#21">Editing records and adding new ones.</a></li>
<li><a href="#4">Queued pdf downloading and text extraction.</a></li>
<li><a href="#5">Searching for keywords in extracted articles.</a></li>
<li><a href="#6">Filtering articles based on keywords in their full
text.</a></li>
<li><a href="#20">Save notes for any article using the inbuilt editor.</a></li>
<li><a href="#7">Using operators on keyword searches.</a></li>
<li><a href="#8">Viewing your personal database in a single-view format.</a></li>
<li><a href="#9">Tagging articles for later referral.</a></li>
<li><a href="#10">Copying interesting article information throughout the
search.</a></li>
<li><a href="#22">Add text and article information for multiple
articles into the session clipboard.</a></li>
<li><a href="#11">Extracting the text from local pdf files.</a></li>
<li><a href="#12">Viewing pdfs of interesting articles.</a></li>
<li><a href="#13">Deleting saved data.</a></li>

</ul>
<br>
<br>
<a NAME="23">
<h2>Three flavors of CitationControl.</h2>
<p>CitationControl until version 1.06 supported searches primarily
from the scopus database. The upcoming version will be available in
three flavors - Pubmed, Scopus and ISI. Install the one you are
interested in (Do not install multiple flavors if you want to avoid
database duplication.) If you have a lot of space and don't mind
having three copies of an article, then it is fine to install all
three versions. The new version 1.07 is currently under development
and will become available in the next week or so. Watch this site for
more details.</p>
</a>
<br>
<br>

</ul>
<br>
<br>
<a NAME="17">
<h2>Starting CitationControl.</h2>
<p>When CitationControl is started, it first checks for an internet
connection and then for access to the Scopus website. If you do not
have access to the scopus website, change your preferences. Without internet access, you can still <a href="#8">access your database</a>, <a href="#15">double
click to open the articles</a>, <a href="#9">tag them</a> or <a href="#16">view their pictures</a>. You
cannot download pdfs, index your local pdfs, get citations and
references or use other functions that require internet access.</p>
</a>
<br>
<br>

<a NAME="1">
<h2>Setting preferences.</h2>
<p>If you are a new user, this is probably going to be the first
step. Go to Edit.Preferences and change values as needed (See window
snapshot below). Values can be reset to the
default by clicking the button below. The
first tab in this window controls how you connect to the scopus
website. You can choose a 'No proxy' or a proxy setting based on your
service provider. If you do choose the proxy setting, make sure that
the proxy address you choose is the actual site (with a port number,
separated by a colon), not the location of the 'pac' file.</p>
<div>
<br>
<img src="Screenshot_preferences1.png" alt="" width="570" height="437">
</div>
<br>

<p>The next tab is 'Storage' (see image below). This is where your stored pdf files,
extracted text and database will be stored. Leave it at the default
value. If you do choose to change it, make sure you choose an
appropriate location with enough space. Also, the browse button may
not work in your system correctly. However, you could directly copy
and paste the new folder location from an explorer window. Keep the
path separators the same as shown below.</p>
<div>
<br>
<img src="Screenshot_preferences2.png" alt="" width="576" height="439">
</div>
<br>

<p>The last tab in preferences is meant for controlling pdf settings (see
image below). The 'save pdfs' button is checked by default. If you
feel that there is not enough space in your storage folder to save
pdfs, then you can uncheck this button. However, you won't be able to
<a href="#15">double click and open a pdf</a> or <a href="#16">view images</a> from the pdf file if you
make this choice. The second button for 'double clicking pdfs' is
artifactual and will be removed in future versions. It has no function
at this point.</p>
<p>In the lower portion for indexing options, you can choose either to
overwrite or mark as duplicates, the pdf files that you come across
during <a href="#14">file indexing</a>. Also, any found files will be tagged with the
path to their original location by default. You can change this to
either tagging with only the parent folder or a custom tag.</p>
<div>
<br>
<img src="Screenshot_preferences3.png" alt="" width="571" height="441">
</div>
<br>
</a>

<a NAME="14">
<h2>Indexing article pdf files in your
computer.</h2>
<p>If you are a first time user, please <a href="#1">update the preferences dialog</a></p>
<p>First time users may find this as one of the most useful
features. If you have a lot of pdfs that are already saved in your
computer, you should index them so that the same pdfs do not need to
be downloaded again. This adds them to your database, from which point
you can either search for references and citations for these articles,
double click to open the pdf, or view and save images in the pdf file
to a local directory. Go to File.Index local pdfs (Alt-f-i) and the
below dialog will be opened.</p>
<p> As a first time user, you could
index all the pdfs in your computer. This is a recommended action
since this avoids having to download the same pdf twice. This will take a long time since
the program goes through every pdf file in your computer, extracts the
text and obtains details of the file (This can taken especially longer
if there are pdf books in your computer). However, you have to do this
only once. Alternatively, if you know that most of your pdfs
are in one location, say the 'Documents' folder, then just choose that
directory using the button on the right. Indexing is done according to
the options that you had previously set. All directories are
recursively checked.</p>
<div>
<br>
<img src="Screenshot_index_pdf_dialog_full_running.png" alt="" width="718" height="596">
</div>
<br> 
<br>
</a>

<a NAME="15">
<h2>Open any pdf file in your database immediately.</h2>
<p>This option is available if you choose to save the pdfs in the
<a href="#1">preferences</a> window (on by default). Just double click a record and
the pdf file opens in your default pdf viewer.</p>
</a>

<a NAME="16">
<h2>Viewing images from articles in the database.</h2>
<p>This is just a utility function. Either right click on any record
that you have a saved pdf of. Click on the 'Display images from this
pdf' option and a picture viewer populated with images from the
selected pdf file will be opened. From here, you can delete
unnecessary images using the delete button or right-clicking an image
and then save the images for later use in presentations (from the menu option).</p>
<div>
<br>
<img src="Screenshot_image_viewer.png" alt="" width="807" height="621">
</div>
<br> 
<br>
</a>

<a NAME="2">
<h2>Performing a scopus search.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p> You can do online searches based on keywords, authors, year ranges
and journals and add articles to your database.</p>
</p>Here are the rules:
<ul>
<li>All search terms are checked in combination, i.e. if you have multiple
search terms, only results that match all of them are obtained and
displayed.</li>
<li>Only 
search terms can be separated by spaces. No other spaces can be
introduced. Author name search terms begin with a: (e.g. a:Wilson,M or
a:Hjelmstad with no spaces in between). The same rules apply for
journal search terms which begin with j: (e.g. j:Neuron,
j:Journal,of,Neuroscience - again no spaces, use commas
instead).</li>
<li>Years are always a range(e.g. y:2008-2010 or
y:2008-2008). Year ranges are exclusive i.e. y:2008-2010 searches only
for articles in 2009, for all three years, enter 'y:2007-2011'. This is a bug, but it will be fixed in the
next version.</li>
</ul>
</p>
<p>Just type in the search terms and hit enter. After a short
pause, progress dialog and a list of the first matching 200 articles will be retrieved. From
here, you can either <a href="#3">get all citations and references</a> for selected
articles, <a href="#10">select articles for later use</a>, or <a href="#4">download the searchable
text</a> and pdfs of all these articles. (See screen shots below)</p>
<div>
<br>
<img src="Screenshot_search1.png" alt="" width="588" height="91">
</div>
<br>
<div>
<br>
<img src="Screenshot_search2.png" alt="" width="464" height="109">
</div>
<br>
<div>
<br>
<img src="Screenshot_search3.png" alt="" width="475" height="100">
</div>
<br>
<div>
<br>
<img src="Screenshot_search_prog_dialog.png" alt="" width="313" height="116">
</div>
<br>
<br>
</a>

<a NAME="3">
<h2>Obtaining citations and references.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>This is one of the strengths of the program, the others being <a href="#14">pdf
indexing</a>, <a href="#4">queued
pdf downloading</a> and searching  <a href="#5">full text of articles</a>. For any selected
article, get all its citations and references. You could do this for
many selected articles rapidly. For this, just select an article and
hit the relevant buttons that appear under the list.</p>
<div>
<br>
<img src="Screenshot_refcite.png" alt="" width="458" height="300">
</div>
<br>
<br>
</a>

<a NAME="18">
<h2>Save and reload sessions of searches.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>Starting from version 1.06, you can save and reopen sessions. All
the information, except the clipboard data, will be saved from the
tabs. This is useful, in practice, if you have a large number of
tabs and searches open and you want to save these tabs into a
file. Opening the session again will allow you to reload your previous
searches and view the relevant lists, even if you are offline.</p>
<p>
<br>
<br>
</a>

<a NAME="19">
<h2>Export all articles to a bibliography file.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>Select the articles you are interested in and export to a .bib file
either by the right click menu, the File menu or 'Ctrl-e'. This file
can then be imported into <a href="http://jabref.sourceforge.net/">Jabref</a>, <a
href="http://www.zotero.org/">zotero</a> or endnote and inserted into the final document
using those tools. Please see the linked websites for how this is
done. This
feature is experimental and suffers from the following caveats.
<ul>
<li>Special characters are not transferred. So you'll need to
either edit the records using the 'Edit records' function or change
them in other programs.</li>
<li>Unpublished articles need to be manually edited.</li>
<li>Issue numbers might be missing in certain records. These need to
be manually added.</li>
</ul></p>
<p>
<br>
<br>
</a>

<a NAME="21">
<h2>Editing records and adding new ones.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>Add new records if they are not found in a web search, for pdfs
that cannot be indexed correctly, and for supplemental information and
errata data. The caveat to using this function is that references and
citations for these articles become unavailable. This function is accessed from the edit menu. The record
adding 
dialog (or the editing dialog) is shown below. To assist with filling in
the details, there is a doi input box. Type or paste in the doi number
of the article and press 'Get Details'. For most doi numbers, the data
is input into the relevant boxes. The title search will also work in
many cases. Alternatively, you can manually enter the information for the
records. Finally, browse and find the pdf file that you
are adding. </p>
<p>Editing works similarly. You can edit records by selecting them in
the database and changing the details. Selecting a new record in the
database changes the details. Hit 'Save' after making any changes.
<div>
<br>
<img src="Screenshot_edit_record.png" alt="" width="725" height="543">
</div>
<br>
<br>
</a>

<a NAME="4">
<h2>Queued pdf downloading and text extraction.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>You can select either a single article or all the articles in the
list. Hit "Obtain Searchable text" and you will see that articles are
starting to download. The program searches for the associated pdf
files, downloads them and then extracts and saves the text. By
default, the
original pdf file is saved. If you feel, you can change this
option. Pdf files can always be downloaded
again as shown <a href="#12">here</a></p>
<div>
<br>
<img src="Screenshot_Obtain_ft.png" alt="" width="683" height="332">
</div>
<br>
<br>
</a>


<a NAME="5">
<h2>Searching for keywords in extracted articles.</h2>
<p>Once you have searchable text, you can either select a number of
articles and check whether a particular phrase occurs in their full
text. If they do exist, then the lines in which these phrases occur
are shown in the text window.</p>
<div>
<br>
<img src="Screenshot_single_search_term.png" alt="" width="696" height="322">
</div>
<br>
<br>
</a>


<a NAME="6">
<h2>Filtering articles based on keywords in their full
text.</h2>
<p>If you select multiple articles and then do a keyword search in the
full text, then only the articles with the keyword or phrase in them
will be highlighted</p>
<div>
<br>
<img src="Screenshot_mult_ft_search_before.png" alt="" width="362" height="461">
</div>
<br>
<br>
<div>
<br>
<img src="Screenshot_mult_ft_search.png" alt="" width="377" height="455">
</div>
<br>
<br>
</a>

<a NAME="20">
<h2>Save notes for any article using the inbuilt editor.</h2>
<p>Write notes on any article using the inbuilt rich text editor (see
picture below). Notes are saved when the save button (Ctrl-s) is
clicked or you move on to a new record.</p>
<div>
<br>
<img src="Screenshot_add_notes.png" alt="" width="735" height="430">
</div>
<br>
<br>
</a>

<a NAME="7">
<h2>Using operators on keyword searches.</h2>
<p>You can also add the operators (and) and (or) while searching for
keywords in a <a href="#5">single article</a> or <a href="#6">multiple
articles.</a> The operator (and) tests whether lines in the chosen
article(s) have both the words in them (e.g. LTP (and) NMDA), whereas
(or) tests for one or the other keyword.
</p>
<div>
<br>
<img src="Screenshot_combine_search_terms.png" alt="" width="365" height="422">
</div>
<br>
<br>
</a>


<a NAME="8">
<h2>Viewing your personal database.</h2>
<p>If you are a first time user, please <a href="#1">update the
preferences dialog</a> and <a href="#14">index the pdf files</a> in your computer</p>
<p>All the data that have been extracted is saved in your personal
database. This is in a folder that you have specified in <a href="#1">
preferences</a>. If you need to conserve space, check the 'Save pdfs'
button in preferences. Each article will then
occupy roughly one tenth the space of a pdf file, saving both space
and processing speed. This personal database can be opened from the
File menu and <a href="#9">tagged</a> for later use.</p>
<div>
<br>
<img src="Screenshot_save_articles.png" alt="" width="452" height="332">
</div>
<br>
<br>
</a>


<a NAME="9">
<h2>Tagging articles for later referral.</h2>
<p>Articles can be tagged. The tags can be deleted and edited. See the
edit menu or the right click menu for further details.</p>
<div>
<br>
<img src="Screenshot_tag.png" alt="" width="428" height="342">
</div>
<br>
<br>
</a>


<a NAME="10">
<h2>Copying interesting articles throughout the
search.</h2>
<p>If any articles interest you, you can add them to the local session
clipboard. All saved articles will be shown when you choose "Show clipboard".</p>
</a>

<a NAME="22">
<h2>Add text and article information for multiple
articles into the session clipboard.</h2>
<p>You can copy the text of any article from the full text window and
add it to the session clipboard using the 'Add text to session
clipboard' option. This will add the text and the article information
to the clipboard, so that when you show the clipboard, it shows both
the selected text and the original article data.</p>
</a>


<a NAME="11">
<h2>Extracting the text from local pdf files.</h2>
<p>Many times the right pdf file cannot be downloaded (You'll see this
as an "x" icon). In such cases,
you might still be able to find it using a google search or through
other sources. You can add these to the database by right clicking the
article and choosing 'Get local pdf file' from the menu.</p>
<div>
<br>
<img src="Screenshot_Obtain_ft.png" alt="" width="683" height="332">
</div>
<br>
<br>
</a>


<a NAME="12">
<h2>Viewing pdfs of interesting articles.</h2>
<p>If you do not have the 'Save pdfs' preference checked and if an article in your database seems interesting, you can download the
article from the web using either the edit menu or a right click on
the desired article.</p>
</a>


<a NAME="13">
<h2>Deleting saved data.</h2>
<p>Saved data can always be deleted from the right-click menu.</p>
</a>


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